AP Syllabus focus:
‘Changes to an enzyme’s molecular structure can alter its function or efficiency within an enzymatic system.’
Enzymes work because their 3D structures position key chemical groups precisely.
This diagram illustrates the induced-fit model, where substrate binding triggers a conformational change that improves active-site complementarity. It highlights how correct alignment of catalytic groups is achieved dynamically, rather than by a perfectly rigid active site. The sequence reinforces why structural shifts can change binding efficiency and reaction rate. Source
When that structure shifts—slightly or dramatically—binding and catalysis can weaken or fail, disrupting the reaction rates cells depend on.
Why structure determines enzyme function
Enzymes are protein catalysts whose activity depends on conformation (their specific 3D shape) and the placement of amino acid side chains that participate in binding and chemical transformation. Structural changes can:
Reduce the probability of productive binding between enzyme and reactant(s)
Misalign catalytic residues, lowering reaction rate
Destabilise the protein so fewer functional molecules exist at any time
Structural stability and the “functional shape”
Protein shape is maintained by many weak interactions (and sometimes covalent links), so enzyme function is inherently sensitive to changes that affect these interactions.
Denaturation: A loss of native protein structure (secondary, tertiary, and/or quaternary) that disrupts normal function, often by altering the geometry and chemistry of catalytic regions.
Even modest conformational shifts can reduce efficiency without fully denaturing the enzyme.
This sequence diagram shows substrates binding to an enzyme, formation of an enzyme–substrate complex, and release of product. The changing enzyme shape emphasizes that catalysis depends on maintaining the correct active-site geometry throughout binding and turnover. It also reinforces that the enzyme can revert to a functional conformation after product release. Source
These graphs connect enzyme activity to temperature by separating two effects: faster molecular motion increases reaction rate, but unfolding (denaturation) reduces the fraction of functional enzyme. The combined result is an intermediate optimum temperature where catalytic throughput is highest. This helps explain why structural stability can matter as much as catalytic chemistry for overall efficiency. Source
Levels of structure that can change
Primary structure (amino acid sequence)
A change in sequence (for example, from a mutation) can:
Replace a charged or polar residue with a nonpolar one, altering local interactions
Remove a residue needed for catalysis or substrate binding
Disrupt folding pathways, increasing misfolding or aggregation
Because higher-level folding depends on the sequence, primary changes can propagate into major 3D rearrangements.
Secondary and tertiary structure
Alterations to α-helices, β-sheets, or overall folding can change the shape and chemical environment of catalytic regions. Common molecular features affected include:
Hydrogen bonds that stabilise helices/sheets
Ionic interactions (salt bridges) that stabilise folds
Hydrophobic interactions that drive core packing
If these interactions shift, residues may no longer be positioned to stabilise transition states, reducing catalytic power.
Quaternary structure (multi-subunit enzymes)
For enzymes made of multiple polypeptides, changes that weaken subunit association can:
Prevent formation of a functional complex
Alter communication between subunits, disrupting coordinated activity
Reduce stability, shortening the enzyme’s functional lifetime in the cell
Common causes of structural change (beyond sequence)
Covalent modification or chemical damage
Enzymes can be altered by chemical reactions that modify side chains:
Oxidation of sensitive residues can change charge or bonding capacity
Unintended covalent modifications can block key residues or distort folding
Disruption of structural cross-links (when present) can reduce rigidity needed for catalysis
These changes often reduce efficiency before complete loss of function is apparent.
Misfolding and aggregation
If folding is incorrect, hydrophobic regions may be exposed, promoting aggregation. Aggregated proteins are typically:
Less soluble
Less available for catalysis
More likely to be targeted for degradation
Loss of required partners (cofactors or prosthetic groups)
Some enzymes require non-protein components to maintain the correct active conformation or chemical capability.
Without the required component, the enzyme may bind reactants weakly or be unable to carry out essential electron transfers or group transfers.
Structural integrity can also decline if the partner normally stabilises the folded state.
How structural change alters efficiency in an enzymatic system
In cells, enzymes operate as parts of enzymatic systems (interconnected pathways and networks). Structural changes can therefore have system-level effects:
Reduced catalytic throughput: fewer product molecules formed per unit time
Bottlenecks in pathways: one weakened step limits overall flux even if other enzymes are intact
Altered regulation: structural changes can impair regulatory regions, causing inappropriate activity levels (too low or uncontrolled)
Partial loss vs complete loss of function
Not all structural change is all-or-nothing:
Partial conformational shifts may decrease reaction rate while retaining some activity
Instability can shorten the time an enzyme stays functional, lowering effective enzyme concentration
Severe deformation can eliminate activity by preventing proper binding or chemistry
Cellular consequences and safeguards linked to structure
Because damaged enzymes can waste resources and disrupt metabolism, cells invest in quality control:
Chaperone proteins help enzymes fold into functional conformations and refold some misfolded proteins
Targeted degradation pathways remove persistently misfolded or damaged enzymes
Compartmentalisation can limit exposure of enzymes to damaging conditions and localise repair/turnover machinery
These safeguards help maintain overall pathway efficiency when individual enzyme molecules lose function due to structural changes.
FAQ
Yes. Small conformational shifts can subtly alter the positioning of catalytic side chains or exclude water/ions differently, lowering $k_{cat}$ or effective binding without destroying the entire fold.
Protein folding is cooperative. A substitution can disrupt a key interaction “node” (e.g., a buried salt bridge), shifting packing elsewhere and indirectly reshaping catalytic regions through long-range structural coupling.
Catalysis often depends on specific residues acting as proton donors/acceptors or stabilising charge. Modifying that residue can leave binding mostly intact but eliminate the chemistry of transition-state stabilisation.
They rely on precise subunit interfaces. Small interface changes can prevent assembly, destabilise the complex, or block conformational communication between subunits needed for full activity.
Quality-control proteins assess exposure of hydrophobic patches and persistence of misfolding. Proteins that repeatedly fail refolding cycles are often tagged for degradation, whereas transiently misfolded proteins may be rescued by chaperones.
Practice Questions
Explain how a change in an enzyme’s tertiary structure can reduce its catalytic activity. (2 marks)
Correctly states that altered 3D shape changes the geometry/chemical environment needed for binding and/or catalysis (1).
Correctly links this to reduced rate (e.g., fewer successful enzyme–substrate interactions or misaligned catalytic residues) (1).
A cell has a mutation in a gene encoding an enzyme used in a metabolic pathway. The mutated enzyme is produced but the pathway’s product concentration falls. Describe how a change in primary structure can lead to decreased pathway output, referring to protein folding and enzyme availability. (5 marks)
States that a mutation changes the amino acid sequence (primary structure) (1).
Explains that altered sequence can disrupt folding/secondary–tertiary interactions (e.g., hydrogen bonds/ionic/hydrophobic packing), changing conformation (1).
Links conformational change to reduced catalytic efficiency (e.g., poorer binding or catalytic residue mispositioning) (1).
Explains misfolding can cause aggregation and/or instability, reducing the number of functional enzyme molecules (1).
Links reduced functional enzyme concentration or lower activity to a bottleneck that decreases pathway product output (1).
